Are you making sure to power off and not just use sleep mode? It uses more power in sleep mode.
Also I have found that if the Kobo is officially 'processing' after the charging/managing it can run the battery right down. After seriously organizing the e-books one day, it 'processed' for HOURS, and when it was finally done, the battery was dead again :P
But after charging it (only, no managing) The battery has lasted properly since then
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